---
name: "spoa"
section: "1"
platform: "linux"
package: "spoa"
version: "4.1.4-2+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/spoa"
---

# spoa(1)

SIMD partial order alignment tool

## NAME

spoa - SIMD partial order alignment tool

## SYNOPSIS

**spoa** \[options ...\] \<sequences\>

## DESCRIPTION

Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to generate consensus sequences (as described in 10.1093/bioinformatics/btg109). It supports three alignment modes: local (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap).

## OPTIONS

\<sequences\>

-

  input file in FASTA/FASTQ format containing sequences

-

  ### Optional

**-m**, **--match** \<int\>

-

  default: 5 score for matching bases

**-x**, **--mismatch** \<int\>

-

  default: **-4** score for mismatching bases

**-g**, **--gap** \<int\>

-

  default: **-8** gap penalty (must be negative)

**-l**, **--algorithm** \<int\>

-

  default: 0 alignment mode:

-

  0 - local (Smith-Waterman) 1 - global (Needleman-Wunsch) 2 - semi-global

**-r**, **--result** \<int\>

-

  default: 0 result mode:

-

  0 - consensus 1 - multiple sequence alignment 2 - 0 & 1

**--version**

-

  prints the version number

**-h**, **--help**

-

  prints the usage

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.